Your favorite web-based Gene List Tool?

[Richard Finney]

The Question is : what are the good WEB tools for telling a story about a list of genes?

Usually I pop on over to David Genesets: http://david.abcc.ncifcrf.gov/ But it's got the norovirus or some other 48 hour type flu and is not working today.

Ideally a good web tool is not just a download a perl or java script and does not require registration or "prove you are a human" interface. A good site will have just "paste the genelist in and press go" interface and your get a sorted list with p (or z or whatever) values and links to more info.

Are there any good "gene list tools" that can identify pathways, common motifs or ontologies that you like and are easy to use???

[biznatch]

I don't have a favourite, but in the last few days I've used:

http://www.informatics.jax.org/batch

http://idconverter.bioinfo.cnio.es/

http://central.biomart.org/

and the UCSC table browser.

Basically I've got about 1200 microarray probesets (about 800 genes) that are attached to some more and some less accurate annotations, and I want to get a unique gene list with accurate mouse gene names and genome coordinates. MGI seems to be the simplest for this task.

[captainentropy]

I also usually use DAVID (and IPA, but that's not free), but since for my work I've found the Panther pathways to be the most helpful, I just go directly to the Panther website.

Here's a new one I've come across that looks to be similar in concept to the other enrichment/pathway tools, but I haven't used it just yet since I got busy with other things.

http://conceptgen.ncibi.org/core/conceptGen/index.jsp

[Richard Finney]

The Concept Gen. Looks interesting. I don't quite get why they want people to log in. I don't think a lot of implementers "get" the concept of "frictionless" in web development. It's too bad people hide cool tools behind login walls.

The panther stuff looks okay. Thanks. Great tables but the Panther Pathways appear to have some very heavy-weight and buggy Java plug-in doing that java "garbage collection" seize-up your machine and have pretty fonts but no actual information type thing going on. It really needs some useability testing. Too bad. Sometimes, I wish people would keep it simple and just give the information in a nice PNG.

[ edit : I remember checking out Panther way back long time ago and the java plugin stuff was a mess ... so I guess it's still a problem ... maybe they can turn it into HTML5 ]

[captainentropy]

Agreed. I'm wondering if since it was developed and hosted at the University of Michigan it's behind a login wall for security/legal reasons?

[Richard Finney]

Right. It's probably a legal requirement. They probably need some "academic only" type deal for KEGG ( or some other resource) and they need to segment their market.